The Lagrangians $$L_\pm:=\frac{1}{2}\left( \dot{q}_1^2\pm\dot{q}_2^2\right)-\frac{1}{2}m^2\left( q_1^2\pm q_2^2\right)$$ each have Euler-Lagrange equations $\ddot{q}_i=-m^2q_i,\,i\in\left\{ 1,\,2\right\}$. The obvious reason is that these equations are uncoupled, so any linear combination of "one-equation" Lagrangians, including these $\pm$ choices, will give the same pair.
The Lagrangian $L_0:=\dot{q}_1\dot{q}_2-m^2q_1q_2$ has the same ELEs as well, so it doesn't couple the $q_i$ even though it looks like it might. What's the physical interpretation of $L_0$ obtaining the same ELEs as $L_+$? It doesn't seem to be of the form $a_+L_++a_-L_-+b+\dot{f}$.
Thinking in terms of Hamiltonians doesn't make it any clearer. With $L_0$ as our choice of Lagrangian, the Hamiltonian is $H_0:=p_1p_2+m^2q_1q_2$, which bears no obvious equivalence to $$H_\pm:=\frac{1}{2}\left( p_1^2\pm p_2^2\right)+\frac{1}{2}m^2\left( q_1^2\pm q_2^2\right)$$ (The momenta have different definitions in terms of the $\dot{q}_i$ in the two cases, but of course we still get the same equations of motion in all cases.)
So is there a more general principle that explains why $L_\pm$ is equivalent to $L_0$, or $H_\pm$ to $H_0$?